From 968810c3e0339a615a3d6f7793eaae29edd47106 Mon Sep 17 00:00:00 2001
From: james94 <james94@mi.fu-berlin.de>
Date: Wed, 24 Aug 2022 09:31:54 +0200
Subject: [PATCH] fix conda
---
Snakefile | 19 +++++++++----------
envs/AUXILIARY_PYTHON_SCRIPTS.yaml | 1 +
envs/UNZIP_and_QC.yaml | 11 ++++++-----
rules/evaluate.smk | 12 ++++++------
4 files changed, 22 insertions(+), 21 deletions(-)
diff --git a/Snakefile b/Snakefile
index 8338c8b..0971ea7 100644
--- a/Snakefile
+++ b/Snakefile
@@ -18,9 +18,9 @@ with open(config['resources'], 'r') as f:
resource = yaml.safe_load(f)
### GET BASENAME FOR READS WILDCARDS ###
-def getBasename4Reads(path):
- base=os.path.basename(path)
- return os.path.splitext(base)[0]
+# def getBasename4Reads(path):
+# base=os.path.basename(path)
+# return os.path.splitext(base)[0]
### CHECK IF INPUT IS GZIPPED ###
def gzipped_or_not(path):
@@ -41,14 +41,13 @@ def genomeSize_auto_or_not(given_size):
return given_size
-def addUniqueLibraryID(library):
- string2Add=library + "_1"
-def to_be_smrtTrimmed(userAnswer):
- if userAnswer == 'True':
- string2Add="smrtTrimmed"
- elif userAnswer == 'False':
- string2Add="notsmrtTrimmed"
+
+ # def to_be_smrtTrimmed(userAnswer):
+ # if userAnswer == 'True':
+ # string2Add="smrtTrimmed"
+ # elif userAnswer == 'False':
+ # string2Add="notsmrtTrimmed"
samples = pd.read_csv(config['samplesTSV'], dtype=str, index_col=False, delim_whitespace=True, skip_blank_lines=True)
if set(['sample', 'Library_R1', 'Library_R2', 'meryl_kmer_size', 'trim10X', 'trimAdapters', 'fastQC']).issubset(samples.columns):
diff --git a/envs/AUXILIARY_PYTHON_SCRIPTS.yaml b/envs/AUXILIARY_PYTHON_SCRIPTS.yaml
index fb91762..06228f8 100644
--- a/envs/AUXILIARY_PYTHON_SCRIPTS.yaml
+++ b/envs/AUXILIARY_PYTHON_SCRIPTS.yaml
@@ -11,3 +11,4 @@ dependencies:
- pandas
- numpy
- ghostscript
+ - python=3.9.*
diff --git a/envs/UNZIP_and_QC.yaml b/envs/UNZIP_and_QC.yaml
index e50ba80..34121fd 100644
--- a/envs/UNZIP_and_QC.yaml
+++ b/envs/UNZIP_and_QC.yaml
@@ -1,11 +1,12 @@
channels:
- anaconda
- - bioconda
- conda-forge
+ - bioconda
dependencies:
- - pigz=2.4
- - trim-galore=0.6.6
- - pandoc=2.11
+ - openssl==3.0.5
+ - python=3.10.5=ha86cf86_0_cpython
+ - pigz=2.6
+ - trim-galore=0.6.7
+ - pandoc=2.11.4
- multiqc=1.9
- - python=3.8.5
- trimmomatic=0.39
diff --git a/rules/evaluate.smk b/rules/evaluate.smk
index 7e81eff..c336a20 100644
--- a/rules/evaluate.smk
+++ b/rules/evaluate.smk
@@ -31,7 +31,7 @@ rule unzipFastq_R1_HiC:
output:
temp(os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R1.fastq")),
log:
- os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip..HiC.R1.{asmID}.log")
+ os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip.HiC.R1.{asmID}.log")
conda:
os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
threads:
@@ -56,7 +56,7 @@ rule symlink_UnzippedFastq_R1_HiC:
None
shell:
"""
- ln -s {input} {output}
+ ln -sf {input} {output}
"""
@@ -94,7 +94,7 @@ rule symlink_UnzippedFastq_R2_HiC:
None
shell:
"""
- ln -s {input} {output}
+ ln -sf {input} {output}
"""
@@ -334,7 +334,7 @@ rule symlink_UnzippedFasta_PRI:
None
shell:
"""
- ln -s {input} {output}
+ ln -fs {input} {output}
"""
################
@@ -350,7 +350,7 @@ rule unzipFasta_ALT:
log:
os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip.ALT.{asmID}.log")
conda:
- os.path.join(workflow.basedir, "envs/pigz.yaml")
+ os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
threads:
resource['unzipFasta_ALT']['threads']
resources:
@@ -431,7 +431,7 @@ rule merqury:
os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell:
"""
- ln -s {input.merylDB_provided} {params.symlink_merylDB}
+ ln -fs {input.merylDB_provided} {params.symlink_merylDB}
cd {params.outPath}
export OMP_NUM_THREADS={threads}
(merqury.sh {params.symlink_merylDB} {input.assemblyPRI} {input.assemblyALT} {params.outFile}) &> {log}
--
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